bucher1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000328) Biomodels notes: Time courses as in figure 2 of the publication. Integration was performed using Copasi 4.6.33. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes.

  • Joachim Bucher
  • Stephan Riedmaier
  • Anke Schnabel
  • Katrin Marcus
  • Gabriele Vacun
  • Thomas S Weiss
  • Wolfgang E Thasler
  • Andreas K Nüssler
  • Ulrich M Zanger
  • Matthias Reuss
BMC Syst Biol 2011; 5 : 66
Abstract
BACKGROUND: The individual character of pharmacokinetics is of great importance in the risk assessment of new drug leads in pharmacological research. Amongst others, it is severely influenced by the properties and inter-individual variability of the enzymes and transporters of the drug detoxification system of the liver. Predicting individual drug biotransformation capacity requires quantitative and detailed models.
RESULTS: In this contribution we present the de novo deterministic modeling of atorvastatin biotransformation based on comprehensive published knowledge on involved metabolic and transport pathways as well as physicochemical properties. The model was evaluated on primary human hepatocytes and parameter identifiability analysis was performed under multiple experimental constraints. Dynamic simulations of atorvastatin biotransformation considering the inter-individual variability of the two major involved enzymes CYP3A4 and UGT1A3 based on quantitative protein expression data in a large human liver bank (n = 150) highlighted the variability in the individual biotransformation profiles and therefore also points to the individuality of pharmacokinetics.
CONCLUSIONS: A dynamic model for the biotransformation of atorvastatin has been developed using quantitative metabolite measurements in primary human hepatocytes. The model comprises kinetics for transport processes and metabolic enzymes as well as population liver expression data allowing us to assess the impact of inter-individual variability of concentrations of key proteins. Application of computational tools for parameter sensitivity analysis enabled us to considerably improve the validity of the model and to create a consistent framework for precise computer-aided simulations in toxicology.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
60.0 second
1e-12 mole
0.001 litre
1e-09 mole litre^(-1.0)
1.6666666666666667e-14 mole second^(-1.0)
1.6666666666666667e-05 litre second^(-1.0)
1.0 dimensionless
Id Name Spatial dimensions Size
cell 3.0 0.0142
compartment 3.0 1.0
medium 3.0 2.0
Id Name Initial quantity Compartment Fixed
ASL_b 0.0 cell
ASL_c 0.0 cell
ASL_m 30.56 medium
ASLoOH_b 0.0 cell
ASLoOH_c 0.0 cell
ASLoOH_m 0.0 medium
ASLpOH_b 0.0 cell
ASLpOH_c 0.0 cell
ASLpOH_m 0.0 medium
AS_b 0.0 cell
AS_c 0.0 cell
AS_m 8797.15 medium
ASoOH_b 0.0 cell
ASoOH_c 0.0 cell
ASoOH_m 0.0 medium
ASpOH_b 0.0 cell
ASpOH_c 0.0 cell
ASpOH_m 0.0 medium

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
ASL_Prot ASL_c > ASL_b

Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASL_c - ASL_b)
ASLoOH_Prot ASLoOH_c > ASLoOH_b

Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASLoOH_c - ASLoOH_b)
ASLpOH_Prot ASLpOH_c > ASLpOH_b

Prot_k1 * ((1 - fu_ASL) / fu_ASL * ASLpOH_c - ASLpOH_b)
AS_Prot AS_c > AS_b

Prot_k1 * ((1 - fu_AS) / fu_AS * AS_c - AS_b)
ASoOH_Prot ASoOH_c > ASoOH_b

Prot_k1 * ((1 - fu_AS) / fu_AS * ASoOH_c - ASoOH_b)
ASpOH_Prot ASpOH_c > ASpOH_b

Prot_k1 * ((1 - fu_AS) / fu_AS * ASpOH_c - ASpOH_b)
CR_oOH ASLoOH_c > ASoOH_c

(k_CR_ASL_c + k_PON_OH_c) * ASLoOH_c
CR_pOH ASLpOH_c > ASpOH_c

(k_CR_ASL_c + k_PON_OH_c) * ASLpOH_c
CYP3A4_ASLoOH ASL_c > ASLoOH_c

CYP3A4_ASLoOH_Vmax / CYP3A4_ASLoOH_Km1 * ASL_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1)
CYP3A4_ASLpOH ASL_c > ASLpOH_c

CYP3A4_ASLpOH_Vmax / CYP3A4_ASLpOH_Km1 * ASL_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1)
CYP3A4_ASoOH AS_c > ASoOH_c

CYP3A4_ASoOH_Vmax / CYP3A4_ASoOH_Km1 * AS_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1)
CYP3A4_ASpOH AS_c > ASpOH_c

CYP3A4_ASpOH_Vmax / CYP3A4_ASpOH_Km1 * AS_c / (1 + AS_c / CYP3A4_ASpOH_Km1 + AS_c / CYP3A4_ASoOH_Km1 + ASL_c / CYP3A4_ASLpOH_Km1 + ASL_c / CYP3A4_ASLoOH_Km1)
Export_AS AS_c > AS_m

Export_AS_k * AS_c
Export_ASL ASL_c > ASL_m

Export_ASL_k * ASL_c
Export_ASLoOH ASLoOH_c > ASLoOH_m

Export_ASLoOH_k * ASLoOH_c
Export_ASLpOH ASLpOH_c > ASLpOH_m

Export_ASLpOH_k * ASLpOH_c
Export_ASoOH ASoOH_c > ASoOH_m

Export_ASoOH_k * ASoOH_c
Export_ASpOH ASpOH_c > ASpOH_m

Export_ASpOH_k * ASpOH_c
Import_AS AS_m > AS_c

Import_AS_k * AS_m
Import_ASL ASL_m > ASL_c

Import_ASL_k * ASL_m
Import_ASLoOH ASLoOH_m > ASLoOH_c

Import_ASLoOH_k * ASLoOH_m
Import_ASLpOH ASLpOH_m > ASLpOH_c

Import_ASLpOH_k * ASLpOH_m
Import_ASoOH ASoOH_m > ASoOH_c

Import_ASoOH_k * ASoOH_m
Import_ASpOH ASpOH_m > ASpOH_c

Import_ASpOH_k * ASpOH_m
R_ASASL_c ASL_c > AS_c

(k_CR_ASL_c + k_PON_ASL_c) * ASL_c
R_ASASL_m ASL_m > AS_m

k_CR_ASL_m * ASL_m
R_oOH_m ASLoOH_m > ASoOH_m

k_CR_ASL_m * ASLoOH_m
R_pOH_m ASLpOH_m > ASpOH_m

k_CR_ASL_m * ASLpOH_m
UGT1A3_AS AS_c > ASL_c

UGT1A3_AS_Vmax * AS_c / (UGT1A3_AS_Km1 + AS_c + AS_c * AS_c / UGT1A3_AS_KI1)

Global parameters

Id Value
CYP3A4_ASLoOH_Km1 3900.0
CYP3A4_ASLoOH_Vmax 39.1342
CYP3A4_ASLpOH_Km1 1400.0
CYP3A4_ASLpOH_Vmax 17.4446
CYP3A4_ASoOH_Km1 29700.0
CYP3A4_ASoOH_Vmax 47.4985
CYP3A4_ASpOH_Km1 25600.0
CYP3A4_ASpOH_Vmax 15.7336
Export_ASL_k 0.021822
Export_ASLoOH_k 0.0026674
Export_ASLpOH_k 0.0011319
Export_AS_k 0.002166
Export_ASoOH_k 0.0015983
Export_ASpOH_k 0.00079526
Import_ASL_k 0.2754
Import_ASLoOH_k 0.026122
Import_ASLpOH_k 0.033729
Import_AS_k 0.020335
Import_ASoOH_k 0.00038875
Import_ASpOH_k 0.0039614
Prot_k1 8.52
UGT1A3_AS_KI1 75000.0
UGT1A3_AS_Km1 12000.0
UGT1A3_AS_Vmax 13.5862
fu_AS 0.22 dimensionless
fu_ASL 0.22 dimensionless
k_CR_ASL_c 0.0000355
k_CR_ASL_m 0.005
k_PON_ASL_c 0.0043734
k_PON_OH_c 0.0039829

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments